Thanks Dan. I tried doing what you suggested, and it didn't work. I verified that I do have full admin rights and that permissions should not be the issue. I decided to try updating via the command prompt and I received the following output below.
I am not sure what it all means and I didn't have time to explore other solutions, so I uninstalled ArcGIS Pro, removed the Pro folder in Program Files\ArcGIS\, and then did a fresh install, which I haven't done since beta! That reset my Python packages back to default and I was able to install the new packages at the current versions and I was able to update one package that had an update. However, there is no another package that needs to be updated, and it won't update. I will restart and see if things get back to normal.
(arcgispro-py3) C:\Program Files\ArcGIS\Pro\bin\Python\envs\arcgispro-py3>conda
update spyder
Fetching package metadata .............
Solving package specifications: .
Package plan for installation in environment C:\Program Files\ArcGIS\Pro\bin\Pyt
hon\envs\arcgispro-py3:
The following NEW packages will be INSTALLED:
pycodestyle: 2.3.1-py35_0
The following packages will be REMOVED:
colorama: 0.3.7-py35_0
pandas: 0.19.2-np111py35_1
py: 1.4.33-py35_0
python: 3.5.3-0
requests: 2.13.0-py35_0
The following packages will be UPDATED:
pyparsing: 2.1.4-py35_0 --> 2.2.0-py35_0
pytest: 3.1.2-py35_0 --> 3.2.1-py35_0
python-dateutil: 2.6.0-py35_0 --> 2.6.1-py35_0
six: 1.10.0-py35_0 --> 1.10.0-py35_1
spyder: 3.1.4-py35_0 --> 3.2.1-py35_0
sympy: 1.0-py35_0 --> 1.1.1-py35_0
Proceed (/n)? y
An unexpected error has occurred.
Please consider posting the following information to the
conda GitHub issue tracker at:
https://github.com/conda/conda/issues
Current conda install:
platform : win-64
conda version : 4.3.16
conda is private : False
conda-env version : 4.3.16
conda-build version : 2.1.8
python version : 3.5.3.final.0
requests version : 2.13.0
root environment : C:\Program Files\ArcGIS\Pro\bin\Python (writable)
default environment : C:\Program Files\ArcGIS\Pro\bin\Python\envs\arcgispro-
py3
envs directories : C:\Program Files\ArcGIS\Pro\bin\Python\envs
C:\Users\jvwhit\AppData\Local\conda\conda\envs
C:\Users\jvwhit\.conda\envs
package cache : C:\Program Files\ArcGIS\Pro\bin\Python\pkgs
C:\Users\jvwhit\AppData\Local\conda\conda\pkgs
channel URLs : https://conda.anaconda.org/esri/win-64
https://conda.anaconda.org/esri/noarch
https://repo.continuum.io/pkgs/free/win-64
https://repo.continuum.io/pkgs/free/noarch
https://repo.continuum.io/pkgs/r/win-64
https://repo.continuum.io/pkgs/r/noarch
https://repo.continuum.io/pkgs/pro/win-64
https://repo.continuum.io/pkgs/pro/noarch
https://repo.continuum.io/pkgs/msys2/win-64
https://repo.continuum.io/pkgs/msys2/noarch
config file : C:\Program Files\ArcGIS\Pro\bin\Python\.condarc
offline mode : False
user-agent : conda/4.3.16 requests/2.13.0 CPython/3.5.3 Windows/7 W
indows/6.1.7601
`$ C:\Program Files\ArcGIS\Pro\bin\Python\envs\arcgispro-py3\Scripts\..\..\..\Sc
ripts\conda update spyder`
Traceback (most recent call last):
File "conda\cli\install.py", line 357, in install
File "conda\plan.py", line 809, in execute_actions
File "conda\instructions.py", line 247, in execute_instructions
File "conda\instructions.py", line 108, in UNLINKLINKTRANSACTION_CMD
File "conda\core\link.py", line 262, in execute
File "conda\core\link.py", line 241, in verify
File "conda\core\link.py", line 155, in prepare
File "conda\core\link.py", line 388, in get_python_version
File "conda\core\linked_data.py", line 147, in get_python_version_for_pref
ix
RuntimeError: multiple python records found in prefix C:\Program Files\ArcGI
S\Pro\bin\Python\envs\arcgispro-py3
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "conda\exceptions.py", line 626, in conda_exception_handler
File "conda\cli\main.py", line 134, in _main
File "conda\cli\main_update.py", line 65, in execute
File "conda\cli\install.py", line 372, in install
conda.exceptions.CondaRuntimeError: Runtime error: RuntimeError: multiple py
thon records found in prefix C:\Program Files\ArcGIS\Pro\bin\Python\envs\arcgisp
ro-py3
(arcgispro-py3) C:\Program Files\ArcGIS\Pro\bin\Python\envs\arcgispro-py3>
: